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Kai Hakala
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An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Y Jiang, TR Oron, WT Clark, AR Bankapur, D D’Andrea, R Lepore, ...
Genome biology 17, 1-19, 2016
4132016
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ...
Genome biology 20, 1-23, 2019
3532019
Large-scale event extraction from literature with multi-level gene normalization
S Van Landeghem, J Björne, CH Wei, K Hakala, S Pyysalo, S Ananiadou, ...
PloS one 8 (4), e55814, 2013
1292013
Biomedical named entity recognition with multilingual BERT
K Hakala, S Pyysalo
Proceedings of the 5th workshop on BioNLP open shared tasks, 56-61, 2019
1042019
Data and systems for medication-related text classification and concept normalization from Twitter: insights from the Social Media Mining for Health (SMM4H)-2017 shared task
A Sarker, M Belousov, J Friedrichs, K Hakala, S Kiritchenko, F Mehryary, ...
Journal of the American Medical Informatics Association 25 (10), 1274-1283, 2018
892018
EVEX in ST’13: Application of a large-scale text mining resource to event extraction and network construction
K Hakala, S Van Landeghem, T Salakoski, Y Van de Peer, F Ginter
Proceedings of the BioNLP shared task 2013 workshop, 26-34, 2013
542013
Exploring biomolecular literature with EVEX: connecting genes through events, homology, and indirect associations
S Van Landeghem, K Hakala, S Rönnqvist, T Salakoski, Y Van de Peer, ...
Advances in bioinformatics 2012, 2012
492012
Syntactic analyses and named entity recognition for PubMed and PubMed Central—up-to-the-minute
K Hakala, S Kaewphan, T Salakoski, F Ginter
Proceedings of the 15th Workshop on Biomedical Natural Language Processing …, 2016
352016
Neural network and random forest models in protein function prediction
K Hakala, S Kaewphan, J Björne, F Mehryary, H Moen, M Tolvanen, ...
IEEE/ACM Transactions on Computational Biology and Bioinformatics 19 (3 …, 2020
252020
UTU: Disease mention recognition and normalization with CRFs and vector space representations
S Kaewphan, K Hakala, F Ginter
Proceedings of the 8th international workshop on semantic evaluation …, 2014
192014
Assisting nurses in care documentation: from automated sentence classification to coherent document structures with subject headings
H Moen, K Hakala, LM Peltonen, HM Matinolli, H Suhonen, K Terho, ...
Journal of Biomedical Semantics 11, 1-12, 2020
182020
Supporting the use of standardized nursing terminologies with automatic subject heading prediction: a comparison of sentence-level text classification methods
H Moen, K Hakala, LM Peltonen, H Suhonen, F Ginter, T Salakoski, ...
Journal of the American Medical Informatics Association 27 (1), 81-88, 2020
162020
Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling
S Kaewphan, K Hakala, N Miekka, T Salakoski, F Ginter
Database 2018, bay096, 2018
152018
End-to-end system for bacteria habitat extraction
F Mehryary, K Hakala, S Kaewphan, J Björne, T Salakoski, F Ginter
BioNLP 2017, 80-90, 2017
142017
Leveraging text repetitions and denoising autoencoders in OCR post-correction
K Hakala, A Vesanto, N Miekka, T Salakoski, F Ginter
arXiv preprint arXiv:1906.10907, 2019
122019
Sharing annotations better: RESTful open annotation
S Pyysalo, J Campos, JM Cejuela, F Ginter, K Hakala, C Li, P Stenetorp, ...
Proceedings of ACL-IJCNLP 2015 System Demonstrations, 91-96, 2015
112015
Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis
K Hakala, S Van Landeghem, T Salakoski, Y Van de Peer, F Ginter
BMC bioinformatics 16, 1-12, 2015
82015
Evaluation of a prototype system that automatically assigns subject headings to nursing narratives using recurrent neural network
H Moen, K Hakala, LM Peltonen, H Suhonen, P Loukasmäki, T Salakoski, ...
Proceedings of the Ninth International Workshop on Health Text Mining and …, 2018
62018
TurkuNLP entry for interactive Bio-ID assignment
S Kaewphan, F Mehryary, K Hakala, T Salakoski, F Ginter
Proceedings of the BioCreative VI Workshop, 32-35, 2017
62017
Combining supervised and unsupervised named entity recognition to detect psychosocial risk factors in occupational health checks
L Uronen, S Salanterä, K Hakala, J Hartiala, H Moen
International Journal of Medical Informatics 160, 104695, 2022
52022
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